Nonpareil statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Nonpareil
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Nonpareil specifications

Information


Unique identifier OMICS_01419
Name Nonpareil
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Version 3.3.1
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Konstantinos Konstantinidis

Additional information


An online version is available at http://enve-omics.ce.gatech.edu/nonpareil/submit

Information


Unique identifier OMICS_01419
Name Nonpareil
Interface Web user interface
Restrictions to use None
Input format FASTA,FASTQ
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Konstantinos Konstantinidis

Additional information


An online version is available at http://enve-omics.ce.gatech.edu/nonpareil/submit

Publication for Nonpareil

Nonpareil citations

 (11)
library_books

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

2018
mSystems
PMCID: 5893860
PMID: 29657970
DOI: 10.1128/mSystems.00039-18

[…] of the high degree of sequence conservation of the rRNA genes ().We have recently presented a method to assess the level of coverage provided by metagenomic data sets by a redundancy-based approach, Nonpareil (). Briefly, Nonpareil estimates the read redundancy in a metagenomic data set by using ungapped alignments of a subset of sequencing reads against the entire metagenome and then applies the […]

library_books

Metabolic capability and in situ activity of microorganisms in an oil reservoir

2018
Microbiome
PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] ight’, 5; trim_tail_left’, 5; entropy threshold, 50; minimum read length of 70 base; maximum replication, 6; maximum ‘n’s, 0) []. The level of coverage of each metagenomic dataset was estimated using Nonpareil with default parameters []. The trimmed reads were independently assembled de novo using SPAdes v3.7.0 with the following parameters ‘--meta -k 33, 45, 61, 71’. The contigs of each metagenom […]

library_books

From virus isolation to metagenome generation for investigating viral diversity in deep sea sediments

2017
Sci Rep
PMCID: 5566222
PMID: 28827715
DOI: 10.1038/s41598-017-08783-4

[…] A) was performed to assess the relationships between the contribution of identified viral genotypes to viral families of the different viromes and environmental characteristics of the study sites.The Nonpareil software was used to compute a diversity index (the Nonpareil index, which has been found to be correlated to other diversity indices used in metagenomics studies) not based on any reference […]

library_books

Assembling metagenomes, one community at a time

2017
BMC Genomics
PMCID: 5502489
PMID: 28693474
DOI: 10.1186/s12864-017-3918-9

[…] cores of less than 20 [−min_qual_mean 20], and removed all sequences contains any ambiguous bases (N) [−ns_max_n 0].After quality filtering, we assessed the level of coverage of each metagenome using Nonpareil, a statistical program that uses read redundancy to estimate sequence coverage []. […]

library_books

Complementary Metaproteomic Approaches to Assess the Bacterioplankton Response toward a Phytoplankton Spring Bloom in the Southern North Sea

2017
Front Microbiol
PMCID: 5364173
PMID: 28392779
DOI: 10.3389/fmicb.2017.00442

[…] apping employing SortMeRNA version 2.0 (). The number of unique sequences per gene was calculated as described previously (). In addition, coverage was determined for the rRNA-depleted datasets using nonpareil version 2.4 (). Corresponding curves were subsequently generated in R (version 3.2.5; R Development Core Team 2014). […]

library_books

Differential Functional Constraints Cause Strain Level Endemism in Polynucleobacter Populations

2016
mSystems
PMCID: 5069759
PMID: 27822527
DOI: 10.1128/mSystems.00003-16

[…] xcluded from further analysis. Metagenome contigs were assigned to various taxonomic levels by NBC Classifier (). Average metagenome coverage and sequence diversity were computed for each sample with Nonpareil () set at default parameters. AGS was computed for each metagenome sample and Polynucleobacter bin with MicrobeCensus (). FragGeneScan () was also used to predict the protein-coding genes ac […]


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Nonpareil institution(s)
Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA; School of Biology, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA
Nonpareil funding source(s)
Supported by U.S. Department of Energy (Award DE-SC0006662) and by U. S. National Science Foundation (Award No 1241046).

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